Biodiversity, Anti-Trypanosomal Activity Screening, and Metabolomic Profiling of Actinomycetes Isolated from Mediterranean Sponges

Abstract

Marine sponge–associated actinomycetes are considered as promising sources for the discovery of novel biologically active compounds. In the present study, a total of 64 actinomycetes were isolated from 12 different marine sponge species that had been collected offshore the islands of Milos and Crete, Greece, eastern Mediterranean. The isolates were affiliated to 23 genera representing 8 different suborders based on nearly full length 16S rRNA gene sequencing. Four putatively novel species belonging to genera Geodermatophilus, Microlunatus, Rhodococcus and Actinomycetospora were identified based on a 16S rRNA gene sequence similarity of < 98.5% to currently described strains. Eight actinomycete isolates showed bioactivities against Trypanosma brucei brucei TC221 with half maximal inhibitory concentration (IC50) values <20 μg/mL. Thirty four isolates from the Milos collection and 12 isolates from the Crete collection were subjected to metabolomic analysis using high resolution LC-MS and NMR for dereplication purposes. Two isolates belonging to the genera Streptomyces (SBT348) and Micromonospora (SBT687) were prioritized based on their distinct chemistry profiles as well as their anti-trypanosomal activities. These findings demonstrated the feasibility and efficacy of utilizing metabolomics tools to prioritize chemically unique strains from microorganism collections and further highlight sponges as rich source for novel and bioactive actinomycetes.

Molecules to Ecosystems: Actinomycete Natural Products In situ

“…Studies have measured the diversity and abundance of actinobacterial symbionts, finding that they are ubiquitously and stably associated within these systems (Abdelmohsen et al, 2014; Braña et al, 2015; Mahmoud and Kalendar, 2016). Subsequently, actinomycetes have been isolated from various sponges and corals to investigate their antimicrobial activities and potential to produce novel bioactive compounds (Schneemann et al, 2010; Cheng et al, 2015; Kuang et al, 2015; Pham et al, 2015; Mahmoud and Kalendar, 2016). The isolates have proved to be a rich source of NP with antifungal, antimicrobial, anti-cancer, and anti-HIV compounds (Abdelmohsen et al, 2014).…”

Metabolomic profiling and biological investigation of the marine sponge‐derived bacterium Rhodococcus sp. UA13

“…A major shortcoming associated with such conventional investigations is the blindness of comprehensive chemical information prior to the laborious isolation work. This is frequently accompanied by the increased possibility of re‐characterisation of known compounds; making the isolation of new chemical entities to some extent an accidental or exceptional event . Likewise, bioassay‐guided isolation, which is commonly followed in natural product discovery, has been also limited by the repeated isolation of known metabolites together with the failure of purifying other trace bioactive constituents.…”

“…In the same way, phylogenetic data based on 16S rRNA gene sequence are not absolutely sufficient in microbial natural product research since related strains do not necessarily exhibit similar chemical profiles, while others belonging to different genera may unpredictably do . For this, metabolomics has growingly attracted a special interest in various aspects of natural products as a powerful and multipurpose approach, having the advantage of simultaneous analysis and characterisation of several active components in complex mixtures without detailed chromatographic work . In view of that, metabolomic profiling based on liquid chromatography mass spectrometry (LC–MS) techniques has emerged as a typical and efficient practice for exploring the chemical complexity of natural sources with limited experimental effort, which in turn allows for cost‐effective drug discovery …”

“…This is frequently accompanied by the increased possibility of re-characterisation of known compounds; making the isolation of new chemical entities to some extent an accidental or exceptional event. 4 Likewise, bioassay-guided isolation, which is commonly followed in natural product discovery, has been also limited by the repeated isolation of known metabolites together with the failure of purifying other trace bioactive constituents. Therefore, the acquired bioactivity data alone might not completely reflect the underlying chemical complexity.…”

“…7 For this, metabolomics has growingly attracted a special interest in various aspects of natural products as a powerful and multipurpose approach, having the advantage of simultaneous analysis and characterisation of several active components in complex mixtures without detailed chromatographic work. 3,4 In view of that, metabolomic profiling based on liquid chromatography mass spectrometry (LC-MS) techniques has emerged as a typical and efficient practice for exploring the chemical complexity of natural sources with limited experimental effort, which in turn allows for cost-effective drug discovery. 7 Thus far, marine sponges have received considerable attention owing to their noteworthy microbial diversity.…”